def get_wf_xas(absorbing_atom, structure, feff_input_set="pymatgen.io.feff.sets.MPXANESSet",
edge="K", radius=10.0, feff_cmd="feff", db_file=None, metadata=None,
user_tag_settings=None, use_primitive=False):
"""
Returns FEFF XANES/EXAFS spectroscopy workflow.
Args:
absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,
then the returned workflow will have fireworks for each absorbing site with the
same symbol.
structure (Structure): input structure
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or spectrum type must be provided
e.g. "pymatgen.io.feff.sets.MPXANESSet" or "XANES"
edge (str): absorption edge. Example: K, L1, L2, L3
radius (float): cluster radius in angstroms. Ignored for K space calculations
feff_cmd (str): path to the feff binary
db_file (str): path to the db file.
metadata (dict): meta data
user_tag_settings (dict): override feff default tag settings
use_primitive (bool): convert the structure to primitive form. This helps to
reduce the number of fireworks in the workflow if the absorbing atom is
specified by its atomic symbol.
Returns:
Workflow
"""
if use_primitive:
structure = structure.get_primitive_structure()
# get the absorbing atom site index/indices
ab_atom_indices = get_absorbing_atom_indices(structure, absorbing_atom)
override_default_feff_params = {"user_tag_settings": user_tag_settings}
spectrum_type = get_feff_input_set_obj(feff_input_set, ab_atom_indices[0], structure).__class__.__name__[2:-3]
# add firework for each absorbing atom site index
fws = []
for ab_idx in ab_atom_indices:
fw_metadata = dict(metadata) if metadata else {}
fw_metadata["absorbing_atom_index"] = ab_idx
fw_name = "{}-{}-{}".format(spectrum_type, edge, ab_idx)
fws.append(XASFW(ab_idx, structure, edge=edge, radius=radius,
feff_input_set=feff_input_set, feff_cmd=feff_cmd, db_file=db_file,
metadata=fw_metadata, name=fw_name,
override_default_feff_params=override_default_feff_params))
wf_metadata = dict(metadata) if metadata else {}
wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
wfname = "{}:{}:{} edge".format(structure.composition.reduced_formula,
"{} spectroscopy".format(spectrum_type), edge)
return Workflow(fws, name=wfname, metadata=wf_metadata)
def __init__(self, absorbing_atom, structure, feff_input_set="ELNES", edge="K", radius=10.,
name="EELS spectroscopy", beam_energy=100, beam_direction=None, collection_angle=1,
convergence_angle=1, user_eels_settings=None, feff_cmd="feff",
override_default_feff_params=None, db_file=None, parents=None, metadata=None,
**kwargs):
"""
Write the input set for FEFF-EELSS spectroscopy, run feff and insert the core-loss spectrum
to the database(or dump to a json file if db_file=None).
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then the entire path to the class or the spectrum type must be provide
e.g. "pymatgen.io.feff.sets.MPELNESSet" or "ELNES"
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
beam_energy (float): Incident beam energy in keV
beam_direction (list): Incident beam direction. If None, the cross section will be averaged.
collection_angle (float): Detector collection angle in mrad.
convergence_angle (float): Beam convergence angle in mrad.
user_eels_settings (dict): override default EELS config. See MPELNESSet.yaml for supported keys.
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
db_file (str): path to the db file.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
feff_input_set = get_feff_input_set_obj(feff_input_set, absorbing_atom, structure, edge,
radius, beam_energy, beam_direction, collection_angle,
convergence_angle, user_eels_settings=user_eels_settings,
**override_default_feff_params)
spectrum_type = feff_input_set.__class__.__name__[2:-3]
t = [WriteFeffFromIOSet(absorbing_atom=absorbing_atom, structure=structure, radius=radius,
feff_input_set=feff_input_set),
RunFeffDirect(feff_cmd=feff_cmd),
PassCalcLocs(name=name),
SpectrumToDbTask(absorbing_atom=absorbing_atom, structure=structure,
db_file=db_file, spectrum_type=spectrum_type, edge=edge,
output_file="eels.dat", metadata=metadata)]
super(EELSFW, self).__init__(t, parents=parents, name="{}-{}".
format(structure.composition.reduced_formula, name), **kwargs)
def __init__(self, absorbing_atom, structure, paths, degeneracies=None, edge="K", radius=10.0,
name="EXAFS Paths", feff_input_set="pymatgen.io.feff.sets.MPEXAFSSet", feff_cmd="feff",
override_default_feff_params=None, parents=None, filepad_file=None, labels=None,
metadata=None, **kwargs):
"""
Write the input set for FEFF-EXAFS spectroscopy with customized scattering paths, run feff,
and insert the scattering amplitude output files(feffNNNN.dat files) to filepad.
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
paths (list): list of paths. A path = list of site indices that defines the path legs.
degeneracies (list): degeneracy of each path.
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
feff_input_set (FeffDictSet)
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
filepad_file (str): path to the filepad config file.
labels (list): list of label used to tag the files inserted into filepad.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
override_default_feff_params.update({"user_tag_settings": {"CONTROL": "0 0 0 0 1 1",
"PRINT": "0 0 0 1 0 3"}})
feff_input_set = get_feff_input_set_obj(feff_input_set, absorbing_atom, structure, edge=edge,
radius=radius, **override_default_feff_params)
t = [CopyFeffOutputs(calc_loc=True),
WriteFeffFromIOSet(absorbing_atom=absorbing_atom, structure=structure, radius=radius,
feff_input_set=feff_input_set),
WriteEXAFSPaths(feff_input_set=feff_input_set, paths=paths, degeneracies=degeneracies),
RunFeffDirect(feff_cmd=feff_cmd),
AddPathsToFilepadTask(filepad_file=filepad_file, labels=labels, metadata=metadata)]
super(EXAFSPathsFW, self).__init__(t, parents=parents, name="{}-{}".format(
structure.composition.reduced_formula, name), **kwargs)
def __init__(self, absorbing_atom, structure, feff_input_set="XANES", edge="K", radius=10.0,
name="XAS spectroscopy", feff_cmd="feff", override_default_feff_params=None,
db_file=None, parents=None, metadata=None, **kwargs):
"""
Write the input set for FEFF-XAS spectroscopy, run FEFF and insert the absorption
coefficient to the database (or dump to a json file if db_file=None).
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or spectrum type must be provided
e.g. "pymatgen.io.feff.sets.MPXANESSet" or "XANES"
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
db_file (str): path to the db file.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
feff_input_set = get_feff_input_set_obj(feff_input_set, absorbing_atom, structure, edge=edge,
radius=radius, **override_default_feff_params)
spectrum_type = feff_input_set.__class__.__name__[2:-3]
t = [WriteFeffFromIOSet(absorbing_atom=absorbing_atom, structure=structure, radius=radius,
feff_input_set=feff_input_set),
RunFeffDirect(feff_cmd=feff_cmd),
PassCalcLocs(name=name),
SpectrumToDbTask(absorbing_atom=absorbing_atom, structure=structure,
db_file=db_file, spectrum_type=spectrum_type, edge=edge,
output_file="xmu.dat", metadata=metadata)]
super(XASFW, self).__init__(t, parents=parents, name="{}-{}".
format(structure.composition.reduced_formula, name), **kwargs)
def get_wf_eels(absorbing_atom,
structure=None,
feff_input_set="pymatgen.io.feff.sets.MPELNESSet",
edge="K",
radius=10.,
beam_energy=100,
beam_direction=None,
collection_angle=1,
convergence_angle=1,
user_eels_settings=None,
user_tag_settings=None,
feff_cmd="feff",
db_file=None,
metadata=None,
use_primitive=False):
"""
Returns FEFF ELNES/EXELFS spectroscopy workflow.
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure. If None and mp_id is provided, the corresponding
structure will be fetched from the Materials Project db.
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or spectrum type must be provided
e.g. "pymatgen.io.feff.sets.MPELNESSet" or "ELNES"
edge (str): absorption edge. K, L1, L2, L3
radius (float): cluster radius in angstroms. Ignored for reciprocal space calculations
beam_energy (float): the incident beam energy in keV
beam_direction (list): incident beam direction. Default is none ==> the spectrum will be
averaged over all directions.
collection_angle (float): collection angle in mrad
convergence_angle (float): convergence angle in mrad
user_eels_settings (dict): override default eels settings.
user_tag_settings (dict): override other general feff default tag settings.
feff_cmd (str): path to the feff binary
db_file (str): path to the db file.
metadata (dict): meta data
use_primitive (bool): convert the structure to primitive form. This helps to
reduce the number of fireworks in the workflow if the absorbing atoms is
specified by its atomic symbol.
Returns:
Workflow
"""
if use_primitive:
structure = structure.get_primitive_structure()
# get the absorbing atom site index/indices
ab_atom_indices = [absorbing_atom] if isinstance(
absorbing_atom, int) else structure.indices_from_symbol(absorbing_atom)
override_default_feff_params = {"user_tag_settings": user_tag_settings}
spectrum_type = get_feff_input_set_obj(feff_input_set, ab_atom_indices[0],
structure).__class__.__name__[2:-3]
# add firework for each absorbing atom site index
fws = []
for ab_idx in ab_atom_indices:
fw_metadata = dict(metadata) if metadata else {}
fw_metadata["absorbing_atom_index"] = ab_idx
fw_name = "{}-{}-{}".format(spectrum_type, edge, ab_idx)
fws.append(
EELSFW(ab_idx,
structure,
feff_input_set=feff_input_set,
edge=edge,
radius=radius,
beam_energy=beam_energy,
beam_direction=beam_direction,
collection_angle=collection_angle,
convergence_angle=convergence_angle,
user_eels_settings=user_eels_settings,
feff_cmd=feff_cmd,
db_file=db_file,
metadata=fw_metadata,
name=fw_name,
override_default_feff_params=override_default_feff_params))
wfname = "{}:{}:{} edge".format(structure.composition.reduced_formula,
"{} spectroscopy".format(spectrum_type),
edge)
wf_metadata = dict(metadata) if metadata else {}
wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
return Workflow(fws, name=wfname, metadata=wf_metadata)
def get_wf_eels(absorbing_atom, structure=None, feff_input_set="pymatgen.io.feff.sets.MPELNESSet",
edge="K", radius=10., beam_energy=100, beam_direction=None, collection_angle=1,
convergence_angle=1, user_eels_settings=None, user_tag_settings=None, feff_cmd="feff",
db_file=None, metadata=None, use_primitive=False):
"""
Returns FEFF ELNES/EXELFS spectroscopy workflow.
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure. If None and mp_id is provided, the corresponding
structure will be fetched from the Materials Project db.
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or spectrum type must be provided
e.g. "pymatgen.io.feff.sets.MPELNESSet" or "ELNES"
edge (str): absorption edge. K, L1, L2, L3
radius (float): cluster radius in angstroms. Ignored for reciprocal space calculations
beam_energy (float): the incident beam energy in keV
beam_direction (list): incident beam direction. Default is none ==> the spectrum will be
averaged over all directions.
collection_angle (float): collection angle in mrad
convergence_angle (float): convergence angle in mrad
user_eels_settings (dict): override default eels settings.
user_tag_settings (dict): override other general feff default tag settings.
feff_cmd (str): path to the feff binary
db_file (str): path to the db file.
metadata (dict): meta data
use_primitive (bool): convert the structure to primitive form. This helps to
reduce the number of fireworks in the workflow if the absorbing atoms is
specified by its atomic symbol.
Returns:
Workflow
"""
if use_primitive:
structure = structure.get_primitive_structure()
# get the absorbing atom site index/indices
ab_atom_indices = get_absorbing_atom_indices(structure, absorbing_atom)
override_default_feff_params = {"user_tag_settings": user_tag_settings}
spectrum_type = get_feff_input_set_obj(feff_input_set, ab_atom_indices[0], structure).__class__.__name__[2:-3]
# add firework for each absorbing atom site index
fws = []
for ab_idx in ab_atom_indices:
fw_metadata = dict(metadata) if metadata else {}
fw_metadata["absorbing_atom_index"] = ab_idx
fw_name = "{}-{}-{}".format(spectrum_type, edge, ab_idx)
fws.append(EELSFW(ab_idx, structure, feff_input_set=feff_input_set, edge=edge, radius=radius,
beam_energy=beam_energy, beam_direction=beam_direction,
collection_angle=collection_angle, convergence_angle=convergence_angle,
user_eels_settings=user_eels_settings, feff_cmd=feff_cmd, db_file=db_file,
metadata=fw_metadata, name=fw_name,
override_default_feff_params=override_default_feff_params))
wfname = "{}:{}:{} edge".format(structure.composition.reduced_formula,
"{} spectroscopy".format(spectrum_type), edge)
wf_metadata = dict(metadata) if metadata else {}
wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
return Workflow(fws, name=wfname, metadata=wf_metadata)
def __init__(self,
absorbing_atom,
structure,
feff_input_set="ELNES",
edge="K",
radius=10.,
name="EELS spectroscopy",
beam_energy=100,
beam_direction=None,
collection_angle=1,
convergence_angle=1,
user_eels_settings=None,
feff_cmd="feff",
override_default_feff_params=None,
db_file=None,
parents=None,
metadata=None,
**kwargs):
"""
Write the input set for FEFF-EELSS spectroscopy, run feff and insert the core-loss spectrum
to the database(or dump to a json file if db_file=None).
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then the entire path to the class or the spectrum type must be provide
e.g. "pymatgen.io.feff.sets.MPELNESSet" or "ELNES"
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
beam_energy (float): Incident beam energy in keV
beam_direction (list): Incident beam direction. If None, the cross section will be averaged.
collection_angle (float): Detector collection angle in mrad.
convergence_angle (float): Beam convergence angle in mrad.
user_eels_settings (dict): override default EELS config. See MPELNESSet.yaml for supported keys.
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
db_file (str): path to the db file.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
feff_input_set = get_feff_input_set_obj(
feff_input_set,
absorbing_atom,
structure,
edge,
radius,
beam_energy,
beam_direction,
collection_angle,
convergence_angle,
user_eels_settings=user_eels_settings,
**override_default_feff_params)
spectrum_type = feff_input_set.__class__.__name__[2:-3]
t = [
WriteFeffFromIOSet(absorbing_atom=absorbing_atom,
structure=structure,
radius=radius,
feff_input_set=feff_input_set),
RunFeffDirect(feff_cmd=feff_cmd),
PassCalcLocs(name=name),
SpectrumToDbTask(absorbing_atom=absorbing_atom,
structure=structure,
db_file=db_file,
spectrum_type=spectrum_type,
edge=edge,
output_file="eels.dat",
metadata=metadata)
]
super(EELSFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
absorbing_atom,
structure,
feff_input_set="XANES",
edge="K",
radius=10.0,
name="XAS spectroscopy",
feff_cmd="feff",
override_default_feff_params=None,
db_file=None,
parents=None,
metadata=None,
**kwargs):
"""
Write the input set for FEFF-XAS spectroscopy, run FEFF and insert the absorption
coefficient to the database (or dump to a json file if db_file=None).
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
then either the entire path to the class or spectrum type must be provided
e.g. "pymatgen.io.feff.sets.MPXANESSet" or "XANES"
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
db_file (str): path to the db file.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
feff_input_set = get_feff_input_set_obj(feff_input_set,
absorbing_atom,
structure,
edge=edge,
radius=radius,
**override_default_feff_params)
spectrum_type = feff_input_set.__class__.__name__[2:-3]
t = [
WriteFeffFromIOSet(absorbing_atom=absorbing_atom,
structure=structure,
radius=radius,
feff_input_set=feff_input_set),
RunFeffDirect(feff_cmd=feff_cmd),
PassCalcLocs(name=name),
SpectrumToDbTask(absorbing_atom=absorbing_atom,
structure=structure,
db_file=db_file,
spectrum_type=spectrum_type,
edge=edge,
output_file="xmu.dat",
metadata=metadata)
]
super(XASFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
absorbing_atom,
structure,
paths,
degeneracies=None,
edge="K",
radius=10.0,
name="EXAFS Paths",
feff_input_set="pymatgen.io.feff.sets.MPEXAFSSet",
feff_cmd="feff",
override_default_feff_params=None,
parents=None,
filepad_file=None,
labels=None,
metadata=None,
**kwargs):
"""
Write the input set for FEFF-EXAFS spectroscopy with customized scattering paths, run feff,
and insert the scattering amplitude output files(feffNNNN.dat files) to filepad.
Args:
absorbing_atom (str): absorbing atom symbol
structure (Structure): input structure
paths (list): list of paths. A path = list of site indices that defines the path legs.
degeneracies (list): degeneracy of each path.
edge (str): absorption edge
radius (float): cluster radius in angstroms
name (str)
feff_input_set (FeffDictSet)
feff_cmd (str): path to the feff binary
override_default_feff_params (dict): override feff tag settings.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
filepad_file (str): path to the filepad config file.
labels (list): list of label used to tag the files inserted into filepad.
metadata (dict): meta data
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_feff_params = override_default_feff_params or {}
override_default_feff_params.update({
"user_tag_settings": {
"CONTROL": "0 0 0 0 1 1",
"PRINT": "0 0 0 1 0 3"
}
})
feff_input_set = get_feff_input_set_obj(feff_input_set,
absorbing_atom,
structure,
edge=edge,
radius=radius,
**override_default_feff_params)
t = [
CopyFeffOutputs(calc_loc=True),
WriteFeffFromIOSet(absorbing_atom=absorbing_atom,
structure=structure,
radius=radius,
feff_input_set=feff_input_set),
WriteEXAFSPaths(feff_input_set=feff_input_set,
paths=paths,
degeneracies=degeneracies),
RunFeffDirect(feff_cmd=feff_cmd),
AddPathsToFilepadTask(filepad_file=filepad_file,
labels=labels,
metadata=metadata)
]
super(EXAFSPathsFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
